I have combined two subsets of two different GSE datasets (One as Controls and One as Cases) and have made a new data frame. I see a complete separation between the two batches. So, I thought I should do the batch correction. But the batch indices and labels completely match. The resulting batch corrected dataset against those labels (which were the batches too) returned no DEGs. Would someone explain why this has happened and how I can get rid of the batch effect for this specific case, please? Thanks in advance.